HHsearch alignment for GI: 254780180 and conserved domain: TIGR03470
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=91.14 E-value=0.41 Score=29.05 Aligned_cols=127 Identities=21% Similarity=0.265 Sum_probs=77.7
Q ss_pred CCCCC-CCCCCCCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHEE---ECHHHHHHHHHHHH
Q ss_conf 56757-400555688789999999997215530378731656657887410135667700077---85999999998753
Q gi|254780180|r 185 AKIQG-SVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHIMHSEIGF---IDAPTAQALNSVKS 260 (360)
Q Consensus 185 A~~~G-SVAAPTAGLHFt~~ll~~L~~kGi~~~~iTLHVG~GTF~Pi~~~~i~~h~mH~E~~~---i~~~~~~~I~~ak~ 260 (360)
T Consensus 96 a~~~g~~v~l~TNG~-Ll~k~i~~~~~~~~~~~~VsLD-G~~-------------e~HD~~r~~~G~Fd~av~aIr~ak~ 160 (318)
T TIGR03470 96 LVARKKFVYLCTNAL-LLEKKLDKFEPSPYLTFSVHLD-GLR-------------EHHDASVCREGVFDRAVEAIREAKA 160 (318)
T ss_pred HHHCCCEEEEECCHH-HHHHHHHHHHHCCCCEEEEECC-CCH-------------HHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 997599799977552-0099999985188836999801-787-------------8866887179779999999999998
Q ss_pred CCCEEEEECHHHHH--HHHHHHHCCCCCCCCCCCCCEEECCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCHHHHHHHHH
Q ss_conf 79809996287899--8999985289846888722366574096114312552775545789999998719899999999
Q gi|254780180|r 261 RGGRIVSVGTTSLR--LLETATTEDGIINPWSGFTNIFITPGYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQ 338 (360)
Q Consensus 261 ~g~rIiAVGTT~~R--~LEs~~~~~~~~~~~~g~T~lfI~Pg~~f~~vd~LiTNFH~P~Stll~Lv~Af~G~~~~~~~Y~ 338 (360)
T Consensus 161 ~G~~V-~iN~Tvf~~~n~~~i~~~~d~~~-~lgVdgi~isp~y~Ye~ap---------~q------~~fl~r~~~~~lfr 223 (318)
T TIGR03470 161 RGFRV-TTNTTLFNDTDPEEVAEFFDYLT-DLGVDGMTISPGYAYEKAP---------DQ------DHFLGRRQTKKLFR 223 (318)
T ss_pred CCCCE-EEEEEEECCCCHHHHHHHHHHHH-HCCCCEEEECCCCCCCCCC---------CC------CCCCCHHHHHHHHH
T ss_conf 69946-79989706899999999999998-7699738976653102376---------31------11158999999999
Q ss_pred HHHHC
Q ss_conf 99986
Q gi|254780180|r 339 HAISH 343 (360)
Q Consensus 339 ~Ai~~ 343 (360)
T Consensus 224 ~il~~ 228 (318)
T TIGR03470 224 EVLSN 228 (318)
T ss_pred HHHHH
T ss_conf 99986